[AMBER] acdoctor: fatal error when reading carboxylates from .mol2 files

From: Niel Henriksen <shireham.gmail.com>
Date: Mon, 1 May 2017 15:09:32 -0700

Hi All,

I haven't used acdoctor before, but now that it is bundled with
antechamber, I'm seeing a possible bug with carboxylate functional groups.
If I read in a structure from a PDB file, generate charges with AM1-BCC,
and write to a Mol2 file, everything seems fine:

$ antechamber -i but.pdb -fi pdb -o but.mol2 -fo mol2 -c bcc -nc -1
... blah blah ...
acdoctor mode has completed checking the input file.
Info: Total number of electrons: 48; net charge: -1
Running: /usr/local/amber16gnu/bin/sqm -O -i sqm.in -o sqm.out

But then if I read in the subsequent Mol2 to convert to another file format
or to even change the atom types, acdoctor gives a fatal error:

$ antechamber -i but.mol2 -fi mol2 -o but.sybyl.mol2 -fo mol2 -at sybyl
... blah blah ...
-- Check Weird Bonds --
/usr/local/amber16gnu/bin/to_be_dispatched/antechamber: Fatal Error!
Weird atomic valence (3) for atom (ID: 1, Name: C1).
       Possible open valence.

The obvious workaround is to disable acdoctor with the '-dr n' flag, but it
seems like acdoctor should be able to handle a carboxylate group .... so
there might be a bug lurking in there somewhere. I've attached the file
used above (but.pdb) to reproduce.


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Received on Mon May 01 2017 - 15:30:02 PDT
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